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Li T, Li S, Kang Y, Zhou J, Yi M. Harnessing the evolving CRISPR/Cas9 for precision oncology. J Transl Med 2024; 22:749. [PMID: 39118151 PMCID: PMC11312220 DOI: 10.1186/s12967-024-05570-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 08/04/2024] [Indexed: 08/10/2024] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/Cas9 system, a groundbreaking innovation in genetic engineering, has revolutionized our approach to surmounting complex diseases, culminating in CASGEVY™ approved for sickle cell anemia. Derived from a microbial immune defense mechanism, CRISPR/Cas9, characterized as precision, maneuverability and universality in gene editing, has been harnessed as a versatile tool for precisely manipulating DNA in mammals. In the process of applying it to practice, the consecutive exploitation of novel orthologs and variants never ceases. It's conducive to understanding the essentialities of diseases, particularly cancer, which is crucial for diagnosis, prevention, and treatment. CRISPR/Cas9 is used not only to investigate tumorous genes functioning but also to model disparate cancers, providing valuable insights into tumor biology, resistance, and immune evasion. Upon cancer therapy, CRISPR/Cas9 is instrumental in developing individual and precise cancer therapies that can selectively activate or deactivate genes within tumor cells, aiming to cripple tumor growth and invasion and sensitize cancer cells to treatments. Furthermore, it facilitates the development of innovative treatments, enhancing the targeting efficiency of reprogrammed immune cells, exemplified by advancements in CAR-T regimen. Beyond therapy, it is a potent tool for screening susceptible genes, offering the possibility of intervening before the tumor initiative or progresses. However, despite its vast potential, the application of CRISPR/Cas9 in cancer research and therapy is accompanied by significant efficacy, efficiency, technical, and safety considerations. Escalating technology innovations are warranted to address these issues. The CRISPR/Cas9 system is revolutionizing cancer research and treatment, opening up new avenues for advancements in our understanding and management of cancers. The integration of this evolving technology into clinical practice promises a new era of precision oncology, with targeted, personalized, and potentially curative therapies for cancer patients.
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Affiliation(s)
- Tianye Li
- Department of Gynecology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, People's Republic of China
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, 310000, People's Republic of China
| | - Shuiquan Li
- Department of Rehabilitation and Traditional Chinese Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, People's Republic of China
| | - Yue Kang
- Department of Obstetrics and Gynecology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Jianwei Zhou
- Department of Gynecology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, People's Republic of China.
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, 310000, People's Republic of China.
| | - Ming Yi
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310000, People's Republic of China.
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2
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Wang J, Gao G, Wang D. Developing AAV-delivered nonsense suppressor tRNAs for neurological disorders. Neurotherapeutics 2024; 21:e00391. [PMID: 38959711 PMCID: PMC11269797 DOI: 10.1016/j.neurot.2024.e00391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/29/2024] [Accepted: 06/19/2024] [Indexed: 07/05/2024] Open
Abstract
Adeno-associated virus (AAV)-based gene therapy is a clinical stage therapeutic modality for neurological disorders. A common genetic defect in myriad monogenic neurological disorders is nonsense mutations that account for about 11% of all human pathogenic mutations. Stop codon readthrough by suppressor transfer RNA (sup-tRNA) has long been sought as a potential gene therapy approach to target nonsense mutations, but hindered by inefficient in vivo delivery. The rapid advances in AAV delivery technology have not only powered gene therapy development but also enabled in vivo preclinical assessment of a range of nucleic acid therapeutics, such as sup-tRNA. Compared with conventional AAV gene therapy that delivers a transgene to produce therapeutic proteins, AAV-delivered sup-tRNA has several advantages, such as small gene sizes and operating within the endogenous gene expression regulation, which are important considerations for treating some neurological disorders. This review will first examine sup-tRNA designs and delivery by AAV vectors. We will then analyze how AAV-delivered sup-tRNA can potentially address some neurological disorders that are challenging to conventional gene therapy, followed by discussing available mouse models of neurological diseases for in vivo preclinical testing. Potential challenges for AAV-delivered sup-tRNA to achieve therapeutic efficacy and safety will also be discussed.
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Affiliation(s)
- Jiaming Wang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
| | - Dan Wang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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3
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Torices L, Nunes-Xavier CE, Mingo J, Luna S, Erramuzpe A, Cortés JM, Pulido R. Induction of Translational Readthrough on Protein Tyrosine Phosphatases Targeted by Premature Termination Codon Mutations in Human Disease. Methods Mol Biol 2024; 2743:1-19. [PMID: 38147205 DOI: 10.1007/978-1-0716-3569-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Nonsense mutations generating premature termination codons (PTCs) in various genes are frequently associated with somatic cancer and hereditary human diseases since PTCs commonly generate truncated proteins with defective or altered function. Induced translational readthrough during protein biosynthesis facilitates the incorporation of an amino acid at the position of a PTC, allowing the synthesis of a complete protein. This may evade the pathological effect of the PTC mutation and provide new therapeutic opportunities. Several protein tyrosine phosphatases (PTPs) genes are targeted by PTC in human disease, the tumor suppressor PTEN being the more prominent paradigm. Here, using PTEN and laforin as examples, two PTPs from the dual-specificity phosphatase subfamily, we describe methodologies to analyze in silico the distribution and frequency of pathogenic PTC in PTP genes. We also summarize laboratory protocols and technical notes to study the induced translational readthrough reconstitution of the synthesis of PTP targeted by PTC in association with disease in cellular models.
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Affiliation(s)
- Leire Torices
- Biobizkaia Health Research Institute, Barakaldo, Spain
| | - Caroline E Nunes-Xavier
- Biobizkaia Health Research Institute, Barakaldo, Spain
- Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Janire Mingo
- Biobizkaia Health Research Institute, Barakaldo, Spain
| | - Sandra Luna
- Biobizkaia Health Research Institute, Barakaldo, Spain
| | - Asier Erramuzpe
- Biobizkaia Health Research Institute, Barakaldo, Spain
- Ikerbasque, The Basque Foundation for Science, Bilbao, Spain
| | - Jesús M Cortés
- Biobizkaia Health Research Institute, Barakaldo, Spain
- Ikerbasque, The Basque Foundation for Science, Bilbao, Spain
- Cell Biology and Histology Department, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Rafael Pulido
- Biobizkaia Health Research Institute, Barakaldo, Spain.
- Ikerbasque, The Basque Foundation for Science, Bilbao, Spain.
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Lu Y, Wu M, Xu Y, Yu L. The Development of p53-Targeted Therapies for Human Cancers. Cancers (Basel) 2023; 15:3560. [PMID: 37509223 PMCID: PMC10377496 DOI: 10.3390/cancers15143560] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
p53 plays a critical role in tumor suppression and is the most frequently mutated gene in human cancers. Most p53 mutants (mutp53) are missense mutations and are thus expressed in human cancers. In human cancers that retain wtp53, the wtp53 activities are downregulated through multiple mechanisms. For example, the overexpression of the negative regulators of p53, MDM2/MDMX, can also efficiently destabilize and inactivate wtp53. Therefore, both wtp53 and mutp53 have become promising and intensively explored therapeutic targets for cancer treatment. Current efforts include the development of small molecule compounds to disrupt the interaction between wtp53 and MDM2/MDMX in human cancers expressing wtp53 and to restore wtp53-like activity to p53 mutants in human cancers expressing mutp53. In addition, a synthetic lethality approach has been applied to identify signaling pathways affected by p53 dysfunction, which, when targeted, can lead to cell death. While an intensive search for p53-targeted cancer therapy has produced potential candidates with encouraging preclinical efficacy data, it remains challenging to develop such drugs with good efficacy and safety profiles. A more in-depth understanding of the mechanisms of action of these p53-targeting drugs will help to overcome these challenges.
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Affiliation(s)
- Yier Lu
- Department of Medical Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Meng Wu
- Department of Medical Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Yang Xu
- Department of Cardiology, The Second Affiliated Hospital, Cardiovascular Key Lab of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou 310009, China
- Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Lili Yu
- Department of Medical Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
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5
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Bez Batti Angulski A, Hosny N, Cohen H, Martin AA, Hahn D, Bauer J, Metzger JM. Duchenne muscular dystrophy: disease mechanism and therapeutic strategies. Front Physiol 2023; 14:1183101. [PMID: 37435300 PMCID: PMC10330733 DOI: 10.3389/fphys.2023.1183101] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/24/2023] [Indexed: 07/13/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe, progressive, and ultimately fatal disease of skeletal muscle wasting, respiratory insufficiency, and cardiomyopathy. The identification of the dystrophin gene as central to DMD pathogenesis has led to the understanding of the muscle membrane and the proteins involved in membrane stability as the focal point of the disease. The lessons learned from decades of research in human genetics, biochemistry, and physiology have culminated in establishing the myriad functionalities of dystrophin in striated muscle biology. Here, we review the pathophysiological basis of DMD and discuss recent progress toward the development of therapeutic strategies for DMD that are currently close to or are in human clinical trials. The first section of the review focuses on DMD and the mechanisms contributing to membrane instability, inflammation, and fibrosis. The second section discusses therapeutic strategies currently used to treat DMD. This includes a focus on outlining the strengths and limitations of approaches directed at correcting the genetic defect through dystrophin gene replacement, modification, repair, and/or a range of dystrophin-independent approaches. The final section highlights the different therapeutic strategies for DMD currently in clinical trials.
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Affiliation(s)
| | | | | | | | | | | | - Joseph M. Metzger
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN, United States
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6
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V M DD, Sivaramakrishnan V, Arvind Kumar K. Structural systems biology approach delineate the functional implications of SNPs in exon junction complex interaction network. J Biomol Struct Dyn 2023; 41:11969-11986. [PMID: 36617892 DOI: 10.1080/07391102.2022.2164355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 12/26/2022] [Indexed: 01/10/2023]
Abstract
In eukaryotes, transcripts that carry premature termination codons (PTC) leading to truncated proteins are degraded by the Nonsense Mediated Decay (NMD) machinery. Missense and nonsense Single Nucleotide Polymorphisms (SNPs) in proteins belonging to Exon junction complex (EJC) and up-frameshift protein (UPF) will compromise NMD leading to the accumulation of truncated proteins in various diseases. The EJC and UPF which are involved in NMD is a good model system to study the effect of SNPs at a system level. Despite the availability of crystal structures, computational tools, and data on mutational and deletion studies, with functional implications, an integrated effort to understand the impact of SNPs at the systems level is lacking. To study the functional consequences of missense SNPs, sequence-based techniques like SIFT and PolyPhen which classify SNPs as deleterious or non-deleterious and structure-based methods like FoldX which calculate the Delta Delta G, (ddGs, ∆∆G) are used. Using FoldX, the ddG for mutations with experimentally validated functional effects is calculated and compared with those calculated for SNPs in the same protein-protein interaction interface. Further, a model is conceived to explain the functional implications of SNPs based on the effects observed for known mutants. The results are visualized in a network format. The effects of nonsense mutations are discerned by comparing with deletion mutation studies and loss of interaction in the crystal structure. The present work not only integrates genomics, proteomics, and classical genetics with 'Structural Biology' but also helps to integrate it into a 'systems-level functional network'.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Datta Darshan V M
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - K Arvind Kumar
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
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Embree CM, Abu-Alhasan R, Singh G. Features and factors that dictate if terminating ribosomes cause or counteract nonsense-mediated mRNA decay. J Biol Chem 2022; 298:102592. [PMID: 36244451 PMCID: PMC9661723 DOI: 10.1016/j.jbc.2022.102592] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a quality control pathway in eukaryotes that continuously monitors mRNA transcripts to ensure truncated polypeptides are not produced. The expression of many normal mRNAs that encode full-length polypeptides is also regulated by this pathway. Such transcript surveillance by NMD is intimately linked to translation termination. When a ribosome terminates translation at a normal termination codon, NMD is not activated, and mRNA can undergo repeated rounds of translation. On the other hand, when translation termination is deemed abnormal, such as that on a premature termination codon, it leads to a series of poorly understood events involving the NMD pathway, which destabilizes the transcript. In this review, we summarize our current understanding of how the NMD machinery interfaces with the translation termination factors to initiate NMD. We also discuss a variety of cis-acting sequence contexts and trans-acting factors that can cause readthrough, ribosome reinitiation, or ribosome frameshifting at stop codons predicted to induce NMD. These alternative outcomes can lead to the ribosome translating downstream of such stop codons and hence the transcript escaping NMD. NMD escape via these mechanisms can have wide-ranging implications on human health, from being exploited by viruses to hijack host cell systems to being harnessed as potential therapeutic possibilities to treat genetic diseases.
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Affiliation(s)
- Caleb M Embree
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio USA
| | - Rabab Abu-Alhasan
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio USA
| | - Guramrit Singh
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio USA.
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8
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2-Guanidino-quinazoline promotes the readthrough of nonsense mutations underlying human genetic diseases. Proc Natl Acad Sci U S A 2022; 119:e2122004119. [PMID: 35994666 PMCID: PMC9436315 DOI: 10.1073/pnas.2122004119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Nonsense mutations account for approximately 11% of all described gene lesions causing human inherited diseases. This premature termination codon (PTC) leads to the premature arrest of translation that generates a truncated peptide and the degradation of the corresponding mRNA through the nonsense-mediated mRNA decay (NMD) pathway. The possibility of restoring the protein expression by promoting PTC readthrough using drugs appears to be an important therapeutic strategy. Unfortunately, this strategy is limited by the small number of molecules known to promote PTC readthrough without affecting normal translation termination. In this work, we identify a new molecule, TLN468, that promotes a high level of PTC readthrough without a detectable effect on normal stop codons. Premature termination codons (PTCs) account for 10 to 20% of genetic diseases in humans. The gene inactivation resulting from PTCs can be counteracted by the use of drugs stimulating PTC readthrough, thereby restoring production of the full-length protein. However, a greater chemical variety of readthrough inducers is required to broaden the medical applications of this therapeutic strategy. In this study, we developed a reporter cell line and performed high-throughput screening (HTS) to identify potential readthrough inducers. After three successive assays, we isolated 2-guanidino-quinazoline (TLN468). We assessed the clinical potential of this drug as a potent readthrough inducer on the 40 PTCs most frequently responsible for Duchenne muscular dystrophy (DMD). We found that TLN468 was more efficient than gentamicin, and acted on a broader range of sequences, without inducing the readthrough of normal stop codons (TC).
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Cheng X, Zhou T, Yang Z, Zhou J, Gao M, Huang Y, Su Z. Premature termination codon: a tunable protein translation approach. Biotechniques 2022; 73:80-89. [PMID: 35796100 DOI: 10.2144/btn-2022-0046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Cellular protein-protein interactions are largely dependent on the activities of signaling proteins. Here, we present a technique to tune gene expression at translation level based on G418-inducible readthrough premature termination codon (PTC-on). To demonstrate how this PTC-on can control the expression level of a cellular signaling protein to regulate signal transduction, we settled a p53 PTC-on system in p53-null H1299 cells. After treating with G418, the cells expressed full-length p53 protein in a dose-dependent manner. We further demonstrated to use this PTC-on approach to dissect p53-dependent and p53-independent apoptosis in response to the DNA double strand breaks in H1299 cells. In principle, the PTC-on can be used as a general approach for exploring the functions of any other signaling proteins.
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Affiliation(s)
- Xiyao Cheng
- School of Light Industry and Food Engineering, Guanxi University, No. 100, Daxuedong Road, Xixiangtang District, Nanning, Guangxi, 530004, China.,Protein Engineering & Biopharmaceutical Sciences Laboratory, Hubei University of Technology, 28 Nanli Road, Wuhan, Hubei, 430068, China
| | - Ting Zhou
- Protein Engineering & Biopharmaceutical Sciences Laboratory, Hubei University of Technology, 28 Nanli Road, Wuhan, Hubei, 430068, China
| | - Zixin Yang
- Protein Engineering & Biopharmaceutical Sciences Laboratory, Hubei University of Technology, 28 Nanli Road, Wuhan, Hubei, 430068, China
| | - Jingjing Zhou
- Protein Engineering & Biopharmaceutical Sciences Laboratory, Hubei University of Technology, 28 Nanli Road, Wuhan, Hubei, 430068, China
| | - Meng Gao
- Protein Engineering & Biopharmaceutical Sciences Laboratory, Hubei University of Technology, 28 Nanli Road, Wuhan, Hubei, 430068, China
| | - Yongqi Huang
- Protein Engineering & Biopharmaceutical Sciences Laboratory, Hubei University of Technology, 28 Nanli Road, Wuhan, Hubei, 430068, China
| | - Zhengding Su
- Protein Engineering & Biopharmaceutical Sciences Laboratory, Hubei University of Technology, 28 Nanli Road, Wuhan, Hubei, 430068, China
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Zhou T, Zhang Y, Chen Y, Shan J, Wang J, Wang Y, Chang J, Jiang W, Chen R, Wang Z, Shi X, Yu Y, Li C, Li X. ROBO1 p.E280* Loses the Inhibitory Effects on the Proliferation and Angiogenesis of Wild-Type ROBO1 in Cholangiocarcinoma by Interrupting SLIT2 Signal. Front Oncol 2022; 12:879963. [PMID: 35615148 PMCID: PMC9124974 DOI: 10.3389/fonc.2022.879963] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
Background Cholangiocarcinoma (CCA) remains one of the most lethal malignancies with an increasing incidence globally. Through whole-exome sequencing of 67 CCA tissues, we identified new mutated genes in CCA, including MACF1, METTL14, ROBO1, and so on. The study was designed to explore the effects and mechanism of ROBO1 wild type (ROBO1WT) and ROBO1E280* mutation on the progression of CCA. Methods Whole-exome sequencing was performed to identify novel mutations in CCAs. In vitro and in vivo experiments were used to examine the function and mechanism of ROBO1WT and ROBO1E280* in cholangiocarcinoma. A tissue microarray including 190 CCA patients and subsequent analyses were performed to indicate the clinical significance of ROBO1. Results Through whole-exome sequencing, we identified a novel CCA-related mutation, ROBO1E280*. ROBO1 was downregulated in CCA tissues, and the downregulation of ROBO1 was significantly correlated with poor prognosis. ROBO1WT suppressed the proliferation and angiogenesis of CCA in vitro and in vivo, while ROBO1E280* lost the inhibitory effects. Mechanically, ROBO1E280* translocated from the cytomembrane to the cytoplasm and interrupted the interaction between SLIT2 and ROBO1. We identified OLFML3 as a potential target of ROBO1 by conducting RNA-Seq assays. OLFML3 expression was downregulated by ROBO1WT and recovered by ROBO1E280*. Functionally, the silence of OLFML3 inhibited CCA proliferation and angiogenesis and was sufficient to repress the loss-of-function role of ROBO1E280*. Conclusions These results suggest that ROBO1 may act as a tumor suppressor and potential prognostic marker for CCA. ROBO1E280* mutation is a loss-of-function mutation, and it might serve as a candidate therapeutic target for CCA patients.
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Affiliation(s)
- Tao Zhou
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yaodong Zhang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yananlan Chen
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jijun Shan
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jifei Wang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yirui Wang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiang Chang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wangjie Jiang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ruixiang Chen
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ziyi Wang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoli Shi
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yue Yu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, National Health Commission (NHC) Key Laboratory of Liver Transplantation, Nanjing, China
| | - Changxian Li
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, National Health Commission (NHC) Key Laboratory of Liver Transplantation, Nanjing, China
- *Correspondence: Xiangcheng Li, ; Changxian Li,
| | - Xiangcheng Li
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, National Health Commission (NHC) Key Laboratory of Liver Transplantation, Nanjing, China
- *Correspondence: Xiangcheng Li, ; Changxian Li,
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11
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Lawson MR, Lessen LN, Wang J, Prabhakar A, Corsepius NC, Green R, Puglisi JD. Mechanisms that ensure speed and fidelity in eukaryotic translation termination. Science 2021; 373:876-882. [PMID: 34413231 PMCID: PMC9017434 DOI: 10.1126/science.abi7801] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/07/2021] [Indexed: 11/02/2022]
Abstract
Translation termination, which liberates a nascent polypeptide from the ribosome specifically at stop codons, must occur accurately and rapidly. We established single-molecule fluorescence assays to track the dynamics of ribosomes and two requisite release factors (eRF1 and eRF3) throughout termination using an in vitro-reconstituted yeast translation system. We found that the two eukaryotic release factors bound together to recognize stop codons rapidly and elicit termination through a tightly regulated, multistep process that resembles transfer RNA selection during translation elongation. Because the release factors are conserved from yeast to humans, the molecular events that underlie yeast translation termination are likely broadly fundamental to eukaryotic protein synthesis.
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Affiliation(s)
- Michael R Lawson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura N Lessen
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Program in Molecular Biophysics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Arjun Prabhakar
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicholas C Corsepius
- Program in Molecular Biophysics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rachel Green
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
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12
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Powers KT, Stevenson-Jones F, Yadav SKN, Amthor B, Bufton JC, Borucu U, Shen D, Becker JP, Lavysh D, Hentze MW, Kulozik AE, Neu-Yilik G, Schaffitzel C. Blasticidin S inhibits mammalian translation and enhances production of protein encoded by nonsense mRNA. Nucleic Acids Res 2021; 49:7665-7679. [PMID: 34157102 PMCID: PMC8287960 DOI: 10.1093/nar/gkab532] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/16/2021] [Accepted: 06/08/2021] [Indexed: 12/14/2022] Open
Abstract
Deciphering translation is of paramount importance for the understanding of many diseases, and antibiotics played a pivotal role in this endeavour. Blasticidin S (BlaS) targets translation by binding to the peptidyl transferase center of the large ribosomal subunit. Using biochemical, structural and cellular approaches, we show here that BlaS inhibits both translation elongation and termination in Mammalia. Bound to mammalian terminating ribosomes, BlaS distorts the 3′CCA tail of the P-site tRNA to a larger extent than previously reported for bacterial ribosomes, thus delaying both, peptide bond formation and peptidyl-tRNA hydrolysis. While BlaS does not inhibit stop codon recognition by the eukaryotic release factor 1 (eRF1), it interferes with eRF1’s accommodation into the peptidyl transferase center and subsequent peptide release. In human cells, BlaS inhibits nonsense-mediated mRNA decay and, at subinhibitory concentrations, modulates translation dynamics at premature termination codons leading to enhanced protein production.
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Affiliation(s)
- Kyle T Powers
- University of Bristol, School of Biochemistry, University Walk, Bristol BS8 1TD, UK
| | | | - Sathish K N Yadav
- University of Bristol, School of Biochemistry, University Walk, Bristol BS8 1TD, UK
| | - Beate Amthor
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ), University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of Heidelberg, Heidelberg, Germany
| | - Joshua C Bufton
- University of Bristol, School of Biochemistry, University Walk, Bristol BS8 1TD, UK
| | - Ufuk Borucu
- University of Bristol, School of Biochemistry, University Walk, Bristol BS8 1TD, UK
| | - Dakang Shen
- University of Bristol, School of Biochemistry, University Walk, Bristol BS8 1TD, UK
| | - Jonas P Becker
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ), University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of Heidelberg, Heidelberg, Germany
| | - Daria Lavysh
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ), University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of Heidelberg, Heidelberg, Germany
| | - Matthias W Hentze
- Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of Heidelberg, Heidelberg, Germany.,European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ), University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of Heidelberg, Heidelberg, Germany
| | - Gabriele Neu-Yilik
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ), University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of Heidelberg, Heidelberg, Germany
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13
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Dmitriev SE, Vladimirov DO, Lashkevich KA. A Quick Guide to Small-Molecule Inhibitors of Eukaryotic Protein Synthesis. BIOCHEMISTRY (MOSCOW) 2021; 85:1389-1421. [PMID: 33280581 PMCID: PMC7689648 DOI: 10.1134/s0006297920110097] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Eukaryotic ribosome and cap-dependent translation are attractive targets in the antitumor, antiviral, anti-inflammatory, and antiparasitic therapies. Currently, a broad array of small-molecule drugs is known that specifically inhibit protein synthesis in eukaryotic cells. Many of them are well-studied ribosome-targeting antibiotics that block translocation, the peptidyl transferase center or the polypeptide exit tunnel, modulate the binding of translation machinery components to the ribosome, and induce miscoding, premature termination or stop codon readthrough. Such inhibitors are widely used as anticancer, anthelmintic and antifungal agents in medicine, as well as fungicides in agriculture. Chemicals that affect the accuracy of stop codon recognition are promising drugs for the nonsense suppression therapy of hereditary diseases and restoration of tumor suppressor function in cancer cells. Other compounds inhibit aminoacyl-tRNA synthetases, translation factors, and components of translation-associated signaling pathways, including mTOR kinase. Some of them have antidepressant, immunosuppressive and geroprotective properties. Translation inhibitors are also used in research for gene expression analysis by ribosome profiling, as well as in cell culture techniques. In this article, we review well-studied and less known inhibitors of eukaryotic protein synthesis (with the exception of mitochondrial and plastid translation) classified by their targets and briefly describe the action mechanisms of these compounds. We also present a continuously updated database (http://eupsic.belozersky.msu.ru/) that currently contains information on 370 inhibitors of eukaryotic protein synthesis.
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Affiliation(s)
- S E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia. .,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - D O Vladimirov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - K A Lashkevich
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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14
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Yang L, Kraft VAN, Pfeiffer S, Merl‐Pham J, Bao X, An Y, Hauck SM, Schick JA. Nonsense-mediated decay factor SMG7 sensitizes cells to TNFα-induced apoptosis via CYLD tumor suppressor and the noncoding oncogene Pvt1. Mol Oncol 2020; 14:2420-2435. [PMID: 32602581 PMCID: PMC7530794 DOI: 10.1002/1878-0261.12754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/18/2020] [Indexed: 12/13/2022] Open
Abstract
Nonsense-mediated decay (NMD) proteins are responsible for the surveillance and degradation of aberrant RNAs. Suppressor with morphogenetic effect on genitalia 7 (SMG7) is an NMD complex protein and a regulator of tumor necrosis factor (TNF)-induced extrinsic apoptosis; however, this unique function has not been explored in detail. In this study, we show that loss of Smg7 leads to unrestricted expression of long noncoding RNAs (lncRNAs) in addition to NMD targets. Functional analysis of Smg7-/- cells showed downregulation of the tumor suppressor cylindromatosis (CYLD) and diminished caspase activity, thereby switching cells to nuclear factor-κB (NF-κB)-mediated protection. This positive relationship between SMG7 and CYLD was found to be widely conserved in human cancer cell lines and renal carcinoma samples from The Cancer Genome Atlas. In addition to CYLD suppression, upregulation of lncRNAs Pvt1 and Adapt33 rendered cells resistant to TNF, while pharmacologic inhibition of NF-κB in Pvt1-overexpressing TNF-resistant cells and Smg7-deficient spheroids re-established TNF-induced lethality. Thus, loss of SMG7 decouples regulation of two separate oncogenic factors with cumulative downstream effects on the NF-κB pathway. The data highlight a novel and specific regulation of oncogenic factors by SMG7 and pinpoint a composite tumor suppressor role in response to TNF.
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Affiliation(s)
- Limeng Yang
- Genetics and Cellular Engineering GroupInstitute of Molecular Toxicology and PharmacologyHelmholtz Zentrum Munich GmbHGerman Research Center for Environmental HealthNeuherbergGermany
| | - Vanessa A. N. Kraft
- Genetics and Cellular Engineering GroupInstitute of Molecular Toxicology and PharmacologyHelmholtz Zentrum Munich GmbHGerman Research Center for Environmental HealthNeuherbergGermany
| | - Susanne Pfeiffer
- Genetics and Cellular Engineering GroupInstitute of Molecular Toxicology and PharmacologyHelmholtz Zentrum Munich GmbHGerman Research Center for Environmental HealthNeuherbergGermany
| | - Juliane Merl‐Pham
- Research Unit Protein ScienceHelmholtz Zentrum Munich GmbHGerman Research Center for Environmental HealthNeuherbergGermany
| | - Xuanwen Bao
- Institute of Radiation BiologyHelmholtz Zentrum Munich GmbHGerman Research Center for Environmental HealthNeuherbergGermany
| | - Yu An
- Department of Chinese MedicineNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Stefanie M. Hauck
- Research Unit Protein ScienceHelmholtz Zentrum Munich GmbHGerman Research Center for Environmental HealthNeuherbergGermany
| | - Joel A. Schick
- Genetics and Cellular Engineering GroupInstitute of Molecular Toxicology and PharmacologyHelmholtz Zentrum Munich GmbHGerman Research Center for Environmental HealthNeuherbergGermany
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15
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Lashkevich KA, Shlyk VI, Kushchenko AS, Gladyshev VN, Alkalaeva EZ, Dmitriev SE. CTELS: A Cell-Free System for the Analysis of Translation Termination Rate. Biomolecules 2020; 10:E911. [PMID: 32560154 PMCID: PMC7356799 DOI: 10.3390/biom10060911] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/29/2020] [Accepted: 06/13/2020] [Indexed: 12/11/2022] Open
Abstract
Translation termination is the final step in protein biosynthesis when the synthesized polypeptide is released from the ribosome. Understanding this complex process is important for treatment of many human disorders caused by nonsense mutations in important genes. Here, we present a new method for the analysis of translation termination rate in cell-free systems, CTELS (for C-terminally extended luciferase-based system). This approach was based on a continuously measured luciferase activity during in vitro translation reaction of two reporter mRNA, one of which encodes a C-terminally extended luciferase. This extension occupies a ribosomal polypeptide tunnel and lets the completely synthesized enzyme be active before translation termination occurs, i.e., when it is still on the ribosome. In contrast, luciferase molecule without the extension emits light only after its release. Comparing the translation dynamics of these two reporters allows visualization of a delay corresponding to the translation termination event. We demonstrated applicability of this approach for investigating the effects of cis- and trans-acting components, including small molecule inhibitors and read-through inducing sequences, on the translation termination rate. With CTELS, we systematically assessed negative effects of decreased 3' UTR length, specifically on termination. We also showed that blasticidin S implements its inhibitory effect on eukaryotic translation system, mostly by affecting elongation, and that an excess of eRF1 termination factor (both the wild-type and a non-catalytic AGQ mutant) can interfere with elongation. Analysis of read-through mechanics with CTELS revealed a transient stalling event at a "leaky" stop codon context, which likely defines the basis of nonsense suppression.
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Affiliation(s)
- Kseniya A. Lashkevich
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (K.A.L.); (V.I.S.); (A.S.K.)
| | - Valeriya I. Shlyk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (K.A.L.); (V.I.S.); (A.S.K.)
- Department of Molecular Biology, Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Artem S. Kushchenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (K.A.L.); (V.I.S.); (A.S.K.)
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
| | - Elena Z. Alkalaeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Sergey E. Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (K.A.L.); (V.I.S.); (A.S.K.)
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
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16
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Crawford DK, Alroy I, Sharpe N, Goddeeris MM, Williams G. ELX-02 Generates Protein via Premature Stop Codon Read-Through without Inducing Native Stop Codon Read-Through Proteins. J Pharmacol Exp Ther 2020; 374:264-272. [PMID: 32376628 DOI: 10.1124/jpet.120.265595] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/30/2020] [Indexed: 12/17/2022] Open
Abstract
ELX-02 is a clinical stage, small-molecule eukaryotic ribosomal selective glycoside acting to induce read-through of premature stop codons (PSCs) that results in translation of full-length protein. However, improved read-through at PSCs has raised the question of whether native stop codon (NSC) fidelity would be impacted. Here, we compare read-through by ELX-02 in PSC and NSC contexts. DMS-114 cells containing a PSC in the TP53 gene were treated with ELX-02 and tested for increased nuclear p53 protein expression while also monitoring two other proteins for NSC read-through. Additionally, blood samples were taken from healthy subjects pre- and post-treatment with ELX-02 (0.3-7.5 mg/kg). These samples were processed to collect white blood cells and then analyzed by western blot to identify native and potentially elongated proteins from NSC read-through. In a separate experiment, lymphocytes cultivated with vehicle or ELX-02 (20 and 100 μg/ml) were subjected to proteomic analysis. We found that ELX-02 produced significant read-through of the PSC found in TP53 mRNA in DMS-114 cells, resulting in increased p53 protein expression and consistent with decreased nonsense-mediated mRNA degradation. NSC read-through protein products were not observed in either DMS-114 cells or in clinical samples from subjects dosed with ELX-02. The number of read-through proteins identified by using proteomic analysis was lower than estimated, and none of the NSC read-through products identified with >2 peptides showed dose-dependent responses to ELX-02. Our results demonstrate significant PSC read-through by ELX-02 with maintained NSC fidelity, thus supporting the therapeutic utility of ELX-02 in diseases resulting from nonsense alleles. SIGNIFICANCE STATEMENT: ELX-02 produces significant read-through of premature stop codons leading to full-length functional protein, demonstrated here by using the R213X mutation in the TP53 gene of DMS-114 cells. In addition, three complementary techniques suggest that ELX-02 does not promote read-through of native stop codons at concentrations that lead to premature stop codon read-through. Thus, ELX-02 may be a potential therapeutic option for nonsense mutation-mediated genetic diseases.
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Affiliation(s)
| | - Iris Alroy
- Eloxx Pharmaceuticals, Inc., Waltham, Massachusetts
| | - Neal Sharpe
- Eloxx Pharmaceuticals, Inc., Waltham, Massachusetts
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17
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Way CM, Lima Cunha D, Moosajee M. Translational readthrough inducing drugs for the treatment of inherited retinal dystrophies. EXPERT REVIEW OF OPHTHALMOLOGY 2020. [DOI: 10.1080/17469899.2020.1762489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Christopher M Way
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, UK
| | - Dulce Lima Cunha
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, UK
| | - Mariya Moosajee
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
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18
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Beißel C, Grosse S, Krebber H. Dbp5/DDX19 between Translational Readthrough and Nonsense Mediated Decay. Int J Mol Sci 2020; 21:ijms21031085. [PMID: 32041247 PMCID: PMC7037193 DOI: 10.3390/ijms21031085] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 01/31/2020] [Accepted: 02/02/2020] [Indexed: 01/21/2023] Open
Abstract
The DEAD-box protein Dbp5 (human DDX19) remodels RNA-protein complexes. Dbp5 functions in ribonucleoprotein export and translation termination. Termination occurs, when the ribosome has reached a stop codon through the Dbp5 mediated delivery of the eukaryotic termination factor eRF1. eRF1 contacts eRF3 upon dissociation of Dbp5, resulting in polypeptide chain release and subsequent ribosomal subunit splitting. Mutations in DBP5 lead to stop codon readthrough, because the eRF1 and eRF3 interaction is not controlled and occurs prematurely. This identifies Dbp5/DDX19 as a possible potent drug target for nonsense suppression therapy. Neurodegenerative diseases and cancer are caused in many cases by the loss of a gene product, because its mRNA contained a premature termination codon (PTC) and is thus eliminated through the nonsense mediated decay (NMD) pathway, which is described in the second half of this review. We discuss translation termination and NMD in the light of Dbp5/DDX19 and subsequently speculate on reducing Dbp5/DDX19 activity to allow readthrough of the PTC and production of a full-length protein to detract the RNA from NMD as a possible treatment for diseases.
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19
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Beißel C, Neumann B, Uhse S, Hampe I, Karki P, Krebber H. Translation termination depends on the sequential ribosomal entry of eRF1 and eRF3. Nucleic Acids Res 2019; 47:4798-4813. [PMID: 30873535 PMCID: PMC6511868 DOI: 10.1093/nar/gkz177] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/28/2019] [Accepted: 03/08/2019] [Indexed: 01/16/2023] Open
Abstract
Translation termination requires eRF1 and eRF3 for polypeptide- and tRNA-release on stop codons. Additionally, Dbp5/DDX19 and Rli1/ABCE1 are required; however, their function in this process is currently unknown. Using a combination of in vivo and in vitro experiments, we show that they regulate a stepwise assembly of the termination complex. Rli1 and eRF3-GDP associate with the ribosome first. Subsequently, Dbp5-ATP delivers eRF1 to the stop codon and in this way prevents a premature access of eRF3. Dbp5 dissociates upon placing eRF1 through ATP-hydrolysis. This in turn enables eRF1 to contact eRF3, as the binding of Dbp5 and eRF3 to eRF1 is mutually exclusive. Defects in the Dbp5-guided eRF1 delivery lead to premature contact and premature dissociation of eRF1 and eRF3 from the ribosome and to subsequent stop codon readthrough. Thus, the stepwise Dbp5-controlled termination complex assembly is essential for regular translation termination events. Our data furthermore suggest a possible role of Dbp5/DDX19 in alternative translation termination events, such as during stress response or in developmental processes, which classifies the helicase as a potential drug target for nonsense suppression therapy to treat cancer and neurodegenerative diseases.
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Affiliation(s)
- Christian Beißel
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Germany
| | - Bettina Neumann
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Germany
| | - Simon Uhse
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Germany
| | - Irene Hampe
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Germany
| | - Prajwal Karki
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Heike Krebber
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Germany
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20
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Campofelice A, Lentini L, Di Leonardo A, Melfi R, Tutone M, Pace A, Pibiri I. Strategies against Nonsense: Oxadiazoles as Translational Readthrough-Inducing Drugs (TRIDs). Int J Mol Sci 2019; 20:ijms20133329. [PMID: 31284579 PMCID: PMC6651739 DOI: 10.3390/ijms20133329] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 12/24/2022] Open
Abstract
This review focuses on the use of oxadiazoles as translational readthrough-inducing drugs (TRIDs) to rescue the functional full-length protein expression in mendelian genetic diseases caused by nonsense mutations. These mutations in specific genes generate premature termination codons (PTCs) responsible for the translation of truncated proteins. After a brief introduction on nonsense mutations and their pathological effects, the features of various classes of TRIDs will be described discussing differences or similarities in their mechanisms of action. Strategies to correct the PTCs will be presented, particularly focusing on a new class of Ataluren-like oxadiazole derivatives in comparison to aminoglycosides. Additionally, recent results on the efficiency of new candidate TRIDs in restoring the production of the cystic fibrosis transmembrane regulator (CFTR) protein will be presented. Finally, a prospectus on complementary strategies to enhance the effect of TRIDs will be illustrated together with a conclusive paragraph about perspectives, opportunities, and caveats in developing small molecules as TRIDs.
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Affiliation(s)
- Ambra Campofelice
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università Degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy
| | - Laura Lentini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università Degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy
| | - Aldo Di Leonardo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università Degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy
| | - Raffaella Melfi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università Degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy
| | - Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università Degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy
| | - Andrea Pace
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università Degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy
| | - Ivana Pibiri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università Degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy.
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21
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Robichaud N, Sonenberg N, Ruggero D, Schneider RJ. Translational Control in Cancer. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032896. [PMID: 29959193 DOI: 10.1101/cshperspect.a032896] [Citation(s) in RCA: 170] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The translation of messenger RNAs (mRNAs) into proteins is a key event in the regulation of gene expression. This is especially true in the cancer setting, as many oncogenes and transforming events are regulated at this level. Cancer-promoting factors that are translationally regulated include cyclins, antiapoptotic factors, proangiogenic factors, regulators of cell metabolism, prometastatic factors, immune modulators, and proteins involved in DNA repair. This review discusses the diverse means by which cancer cells deregulate and reprogram translation, and the resulting oncogenic impacts, providing insights into the complexity of translational control in cancer and its targeting for cancer therapy.
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Affiliation(s)
- Nathaniel Robichaud
- Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Nahum Sonenberg
- Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Davide Ruggero
- Helen Diller Family Comprehensive Cancer Center, and Departments of Urology and of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158
| | - Robert J Schneider
- NYU School of Medicine, Alexandria Center for Life Science, New York, New York 10016
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22
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Ferguson MW, Gerak CAN, Chow CCT, Rastelli EJ, Elmore KE, Stahl F, Hosseini-Farahabadi S, Baradaran-Heravi A, Coltart DM, Roberge M. The antimalarial drug mefloquine enhances TP53 premature termination codon readthrough by aminoglycoside G418. PLoS One 2019; 14:e0216423. [PMID: 31120902 PMCID: PMC6532957 DOI: 10.1371/journal.pone.0216423] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/19/2019] [Indexed: 11/23/2022] Open
Abstract
Nonsense mutations constitute ~10% of TP53 mutations in cancer. They introduce a premature termination codon that gives rise to truncated p53 protein with impaired function. The aminoglycoside G418 can induce TP53 premature termination codon readthrough and thus increase cellular levels of full-length protein. Small molecule phthalimide derivatives that can enhance the readthrough activity of G418 have also been described. To determine whether readthrough enhancers exist among drugs that are already approved for use in humans, we tested seven antimalarial drugs for readthrough of the common R213X TP53 nonsense mutation in HDQ-P1 breast cancer cells. Mefloquine induced no TP53 readthrough activity as a single agent but it strongly potentiated readthrough by G418. The two enantiomers composing pharmaceutical mefloquine potentiated readthrough to similar levels in HDQ-P1 cells and also in SW900, NCI-H1688 and HCC1937 cancer cells with different TP53 nonsense mutations. Exposure to G418 and mefloquine increased p53 phosphorylation at Ser15 and P21 transcript levels following DNA damage, indicating p53 produced via readthrough was functional. Mefloquine does not appear to enhance readthrough via lysosomotropic effects as it did not significantly affect lysosomal pH, the cellular levels of G418 or its distribution in organellar or cytosolic fractions. The availability of a readthrough enhancer that is already approved for use in humans should facilitate study of the therapeutic potential of TP53 readthrough in preclinical cancer models.
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Affiliation(s)
- Michael W. Ferguson
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chloe A. N. Gerak
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christalle C. T. Chow
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ettore J. Rastelli
- Department of Chemistry, University of Houston, Houston, Texas, United States of America
| | - Kyle E. Elmore
- Department of Chemistry, University of Houston, Houston, Texas, United States of America
| | - Florian Stahl
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sara Hosseini-Farahabadi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alireza Baradaran-Heravi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Don M. Coltart
- Department of Chemistry, University of Houston, Houston, Texas, United States of America
| | - Michel Roberge
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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Tutone M, Pibiri I, Lentini L, Pace A, Almerico AM. Deciphering the Nonsense Readthrough Mechanism of Action of Ataluren: An in Silico Compared Study. ACS Med Chem Lett 2019; 10:522-527. [PMID: 30996790 DOI: 10.1021/acsmedchemlett.8b00558] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/07/2019] [Indexed: 12/26/2022] Open
Abstract
Ataluren was reported to suppress nonsense mutations by promoting the readthrough of premature stop codons, although its mechanism of action (MOA) is still debated. The likely interaction of Ataluren with CFTR-mRNA has been previously studied by molecular dynamics. In this work we extended the modeling of Ataluren's MOA by complementary computational approaches such as induced fit docking (IFD), quantum polarized ligand docking (QPLD), MM-GBSA free-energy calculations, and computational mutagenesis. In addition to CFTR-mRNA, this study considered other model targets implicated in the translation process, such as eukaryotic rRNA 18S, prokaryotic rRNA 16S, and eukaryotic Release Factor 1 (eRF1), and we performed a comparison with a new promising Ataluren analogue (NV2445) and with a series of aminoglycosides, known to suppress the normal proofreading function of the ribosome. Results confirmed mRNA as the most likely candidate target for Ataluren and its analogue, and binding energies calculated after computational mutagenesis highlighted how Ataluren's interaction with the premature stop codon could be affected by ancillary nucleotides in the genetic context.
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Affiliation(s)
- Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF) Università degli Studi di Palermo, via Archirafi 28 - viale delle Scienze, Edificio 16 & 17, 90100-Palermo-Italy
| | - Ivana Pibiri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF) Università degli Studi di Palermo, via Archirafi 28 - viale delle Scienze, Edificio 16 & 17, 90100-Palermo-Italy
| | - Laura Lentini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF) Università degli Studi di Palermo, via Archirafi 28 - viale delle Scienze, Edificio 16 & 17, 90100-Palermo-Italy
| | - Andrea Pace
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF) Università degli Studi di Palermo, via Archirafi 28 - viale delle Scienze, Edificio 16 & 17, 90100-Palermo-Italy
| | - Anna Maria Almerico
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF) Università degli Studi di Palermo, via Archirafi 28 - viale delle Scienze, Edificio 16 & 17, 90100-Palermo-Italy
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Leubitz A, Frydman-Marom A, Sharpe N, van Duzer J, Campbell KCM, Vanhoutte F. Safety, Tolerability, and Pharmacokinetics of Single Ascending Doses of ELX-02, a Potential Treatment for Genetic Disorders Caused by Nonsense Mutations, in Healthy Volunteers. Clin Pharmacol Drug Dev 2019; 8:984-994. [PMID: 30650260 DOI: 10.1002/cpdd.647] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/03/2018] [Indexed: 12/13/2022]
Abstract
ELX-02 is an investigational synthetic eukaryotic ribosome-selective glycoside optimized as a translational read-through molecule that induces read through of nonsense mutations, resulting in normally localized full-length functional proteins. ELX-02 is being developed as a therapy for genetic diseases caused by nonsense mutations. Two phase 1a, randomized, double-blind placebo-controlled, single-ascending-dose studies were conducted in healthy human subjects to evaluate the safety and pharmacokinetics of ELX-02. Single subcutaneously injected doses of ELX-02 between 0.3 mg/kg and 7.5 mg/kg showed an acceptable safety profile without severe or serious drug-related adverse events, including a lack of renal and ototoxicity events. Injection of ELX-02 resulted in a rapid time to peak concentration and elimination phase, with complete elimination from the vascular compartment within 10 hours. ELX-02 area under the concentration-time curve to infinity showed dose-exposure linearity (24-fold increase for a 25-fold dose increase), and the maximum concentration showed dose proportionality (17-fold increase for a 25-fold increase). The mean apparent volume of distribution was dose dependent, suggesting an increased distribution and tissue uptake of ELX-02 at higher doses. The primary route of excretion was in the urine, with the majority of the compound excreted unchanged. These results support the evaluation of the safety, pharmacokinetics, and efficacy of repeat dosing in future studies.
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25
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Young R, Purton S. CITRIC: cold-inducible translational readthrough in the chloroplast of Chlamydomonas reinhardtii using a novel temperature-sensitive transfer RNA. Microb Cell Fact 2018; 17:186. [PMID: 30474564 PMCID: PMC6260665 DOI: 10.1186/s12934-018-1033-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/16/2018] [Indexed: 01/17/2023] Open
Abstract
Background The chloroplast of eukaryotic microalgae such as Chlamydomonas reinhardtii is a potential platform for metabolic engineering and the production of recombinant proteins. In industrial biotechnology, inducible expression is often used so that the translation or function of the heterologous protein does not interfere with biomass accumulation during the growth stage. However, the existing systems used in bacterial or fungal platforms do not transfer well to the microalgal chloroplast. We sought to develop a simple inducible expression system for the microalgal chloroplast, exploiting an unused stop codon (TGA) in the plastid genome. We have previously shown that this codon can be translated as tryptophan when we introduce into the chloroplast genome a trnWUCA gene encoding a plastidial transfer RNA with a modified anticodon sequence, UCA. Results A mutated version of our trnWUCA gene was developed that encodes a temperature-sensitive variant of the tRNA. This allows transgenes that have been modified to contain one or more internal TGA codons to be translated differentially according to the culture temperature, with a gradient of recombinant protein accumulation from 35 °C (low/off) to 15 °C (high). We have named this the CITRIC system, an acronym for cold-inducible translational readthrough in chloroplasts. The exact induction behaviour can be tailored by altering the number of TGA codons within the transgene. Conclusions CITRIC adds to the suite of genetic engineering tools available for the microalgal chloroplast, allowing a greater degree of control over the timing of heterologous protein expression. It could also be used as a heat-repressible system for studying the function of essential native genes in the chloroplast. The genetic components of CITRIC are entirely plastid-based, so no engineering of the nuclear genome is required. Electronic supplementary material The online version of this article (10.1186/s12934-018-1033-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rosanna Young
- Algal Research Group, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.,Department of Medicine, Sir Alexander Fleming Building, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Saul Purton
- Algal Research Group, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.
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26
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Zhou J, Qiu C, Pi N, Li S, Cheng X, Zhang L, Chen Y, Huang Y, Sun Y, Su Z. A Protein Biosynthesis Machinery Strategy for Identifying P53 PTC
-Rescuing Compounds as Synergic Anti-Tumor Drugs. ChemistrySelect 2018. [DOI: 10.1002/slct.201802635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jingjing Zhou
- Department of Biotechnology; Hubei University of Technology, Wuhan, Hubei; 430068 P. R. China
| | - Chengbin Qiu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education and Wuhan University; School of Pharmaceutical Sciences Wuhan; Hubei 430071 P. R. China
| | - Ni Pi
- Department of Biotechnology; Hubei University of Technology, Wuhan, Hubei; 430068 P. R. China
| | - Sicong Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education and Wuhan University; School of Pharmaceutical Sciences Wuhan; Hubei 430071 P. R. China
| | - Xiyao Cheng
- Department of Biotechnology; Hubei University of Technology, Wuhan, Hubei; 430068 P. R. China
| | - Lei Zhang
- Department of Biotechnology; Hubei University of Technology, Wuhan, Hubei; 430068 P. R. China
| | - Yao Chen
- Department of Biotechnology; Hubei University of Technology, Wuhan, Hubei; 430068 P. R. China
| | - Yongqi Huang
- Department of Biotechnology; Hubei University of Technology, Wuhan, Hubei; 430068 P. R. China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education and Wuhan University; School of Pharmaceutical Sciences Wuhan; Hubei 430071 P. R. China
| | - Zhengding Su
- Department of Biotechnology; Hubei University of Technology, Wuhan, Hubei; 430068 P. R. China
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Cheruiyot A, Li S, Nickless A, Roth R, Fitzpatrick JAJ, You Z. Compound C inhibits nonsense-mediated RNA decay independently of AMPK. PLoS One 2018; 13:e0204978. [PMID: 30289931 PMCID: PMC6173407 DOI: 10.1371/journal.pone.0204978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 09/18/2018] [Indexed: 12/26/2022] Open
Abstract
The nonsense mediated RNA decay (NMD) pathway safeguards the integrity of the transcriptome by targeting mRNAs with premature translation termination codons (PTCs) for degradation. It also regulates gene expression by degrading a large number of non-mutant RNAs (including mRNAs and noncoding RNAs) that bear NMD-inducing features. Consequently, NMD has been shown to influence development, cellular response to stress, and clinical outcome of many genetic diseases. Small molecules that can modulate NMD activity provide critical tools for understanding the mechanism and physiological functions of NMD, and they also offer potential means for treating certain genetic diseases and cancer. Therefore, there is an intense interest in identifying small-molecule NMD inhibitors or enhancers. It was previously reported that both inhibition of NMD and treatment with the AMPK-selective inhibitor Compound C (CC) induce autophagy in human cells, raising the possibility that CC may be capable of inhibiting NMD. Here we show that CC indeed has a NMD-inhibitory activity. Inhibition of NMD by CC is, however, independent of AMPK activity. As a competitive ATP analog, CC does not affect the kinase activity of SMG1, an essential NMD factor and the only known kinase in the NMD pathway. However, CC treatment down-regulates the protein levels of several NMD factors. The induction of autophagy by CC treatment is independent of ATF4, a NMD target that has been shown to promote autophagy in response to NMD inhibition. Our results reveal a new activity of CC as a NMD inhibitor, which has implications for its use in basic research and drug development.
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Affiliation(s)
- Abigael Cheruiyot
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Shan Li
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Andrew Nickless
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Robyn Roth
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - James A. J. Fitzpatrick
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Biomedical Engineering Washington University, St. Louis, Missouri, United States of America
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Zhongsheng You
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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28
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Campbell MB, Campbell WC, Rogers J, Rogers N, Rogers Z, van den Hurk AM, Webb A, Webb T, Zaslaw P. Bloom syndrome: research and data priorities for the development of precision medicine as identified by some affected families. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a002816. [PMID: 29610394 PMCID: PMC5880269 DOI: 10.1101/mcs.a002816] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bloom syndrome (BS) is a rare, autosomal recessive genetic disorder characterized by short stature, a skin rash associated with sun exposure, and an elevated likelihood of developing cancers of essentially all types, beginning at an early age. Cancer is the leading cause of death for persons with BS, and its early onset results in a reported median lifespan of <30 years. With fewer than 300 documented cases since BS was first described in 1954, its rarity has challenged progress in advancing both the care of and the cure for persons with BS. Presently, there are no known clinically actionable targets specific to persons with this cancer predisposition syndrome, despite the fact that standard cancer treatments are often contraindicated or must be substantially modified for persons with BS. Herein, Zachary Rogers recounts his experience as a cancer patient with BS contemplating a substantially customized chemotherapy regimen that highlights the need for development of individualized treatments in the BS community. We also outline a patient-centered research and community action road map with the goal of improving and prolonging the lives of persons with Bloom syndrome, including the facilitation of precision medicine development specific to this condition.
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Affiliation(s)
- Mary Beth Campbell
- 2017 Pediatric Cancer Nanocourse, Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA.,Caltech Office of Technology Transfer and Corporate Partnerships, California Institute of Technology, Pasadena, California 91125, USA
| | - Wesley C Campbell
- 2017 Pediatric Cancer Nanocourse, Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA.,Department of Physics & Astronomy, University of California Los Angeles, Los Angeles, California 90095, USA
| | - James Rogers
- 2017 Pediatric Cancer Nanocourse, Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | - Natalie Rogers
- 2017 Pediatric Cancer Nanocourse, Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | - Zachary Rogers
- 2017 Pediatric Cancer Nanocourse, Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | - Anne Marie van den Hurk
- 2017 Pediatric Cancer Nanocourse, Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | - Annie Webb
- 2017 Pediatric Cancer Nanocourse, Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | - Talon Webb
- 2017 Pediatric Cancer Nanocourse, Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | - Paul Zaslaw
- 2017 Pediatric Cancer Nanocourse, Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
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Abstract
The tumour suppressor gene TP53 is the most frequently mutated gene in cancer. Wild-type p53 can suppress tumour development by multiple pathways. However, mutation of TP53 and the resultant inactivation of p53 allow evasion of tumour cell death and rapid tumour progression. The high frequency of TP53 mutation in tumours has prompted efforts to restore normal function of mutant p53 and thereby trigger tumour cell death and tumour elimination. Small molecules that can reactivate missense-mutant p53 protein have been identified by different strategies, and two compounds are being tested in clinical trials. Novel approaches for targeting TP53 nonsense mutations are also underway. This Review discusses recent progress in pharmacological reactivation of mutant p53 and highlights problems and promises with these strategies.
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Affiliation(s)
- Vladimir J N Bykov
- Karolinska Institutet, Department of Oncology-Pathology, Cancer Center Karolinska (CCK), SE-171 77 Stockholm, Sweden
| | - Sofi E Eriksson
- Karolinska Institutet, Department of Oncology-Pathology, Cancer Center Karolinska (CCK), SE-171 77 Stockholm, Sweden
| | - Julie Bianchi
- Karolinska Institutet, Department of Oncology-Pathology, Cancer Center Karolinska (CCK), SE-171 77 Stockholm, Sweden
| | - Klas G Wiman
- Karolinska Institutet, Department of Oncology-Pathology, Cancer Center Karolinska (CCK), SE-171 77 Stockholm, Sweden
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30
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Jia P, Zhao Z. Impacts of somatic mutations on gene expression: an association perspective. Brief Bioinform 2017; 18:413-425. [PMID: 27127206 DOI: 10.1093/bib/bbw037] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Indexed: 12/28/2022] Open
Abstract
Assessing the functional impacts of somatic mutations in cancer genomes is critical for both identifying driver mutations and developing molecular targeted therapies. Currently, it remains a fundamental challenge to distinguish the patterns through which mutations execute their biological effects and to infer biological mechanisms underlying these patterns. To this end, we systematically studied the association between somatic mutations in protein-coding regions and expression profiles, which represents an indirect measurement of impacts. We defined mutation features (mutation type, cluster and status) and built linear regression models to assess mutation associations with mRNA expression and protein expression. Our results presented a comprehensive landscape of the associations between mutation features and expression profile in multiple cancer types, including 62 genes showing mutation type associated expression changes, 21 genes showing mutation cluster associations and 51 genes showing mutation status associations. We revealed four characteristics of the patterns that mutations impact on expression. First, we showed that mutation type (truncation versus amino acid-altering mutations) was the most important determinant of expression levels. Second, we detected mutation clusters in well-studied oncogenes that were associated with gene expression. Third, we found both similarities and differences in association patterns existed within and across cancer types. Fourth, although many of the observed associations stay stable at both mRNA and protein expression levels, there are also novel associations uniquely observed at the protein level, which warrant future investigation. Taken together, our findings provided implications for cancer driver gene prioritization and insights into the functional consequences of somatic mutations.
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Abstract
Aminoglycosides are well known as antibiotics that target the bacterial ribosome. However, they also impact the eukaryotic translation mechanism to promote read-through of premature termination codons (PTCs) in mRNA. Aminoglycosides are therefore considered as potential therapies for PTC-associated human diseases. Here, we performed a comprehensive study of the mechanism of action of aminoglycosides in eukaryotes by applying a combination of structural and functional approaches. Our findings reveal complex interactions of aminoglycosides with eukaryotic 80S ribosome caused by their multiple binding sites, which lead to inhibition of intersubunit movement within the human ribosome that impact nearly every aspect of protein synthesis. Aminoglycosides are chemically diverse, broad-spectrum antibiotics that target functional centers within the bacterial ribosome to impact all four principle stages (initiation, elongation, termination, and recycling) of the translation mechanism. The propensity of aminoglycosides to induce miscoding errors that suppress the termination of protein synthesis supports their potential as therapeutic interventions in human diseases associated with premature termination codons (PTCs). However, the sites of interaction of aminoglycosides with the eukaryotic ribosome and their modes of action in eukaryotic translation remain largely unexplored. Here, we use the combination of X-ray crystallography and single-molecule FRET analysis to reveal the interactions of distinct classes of aminoglycosides with the 80S eukaryotic ribosome. Crystal structures of the 80S ribosome in complex with paromomycin, geneticin (G418), gentamicin, and TC007, solved at 3.3- to 3.7-Å resolution, reveal multiple aminoglycoside-binding sites within the large and small subunits, wherein the 6′-hydroxyl substituent in ring I serves as a key determinant of binding to the canonical eukaryotic ribosomal decoding center. Multivalent binding interactions with the human ribosome are also evidenced through their capacity to affect large-scale conformational dynamics within the pretranslocation complex that contribute to multiple aspects of the translation mechanism. The distinct impacts of the aminoglycosides examined suggest that their chemical composition and distinct modes of interaction with the ribosome influence PTC read-through efficiency. These findings provide structural and functional insights into aminoglycoside-induced impacts on the eukaryotic ribosome and implicate pleiotropic mechanisms of action beyond decoding.
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32
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Phylogenetically Conserved Sequences Around Myelin P0 Stop Codon are Essential for Translational Readthrough to Produce L-MPZ. Neurochem Res 2017; 43:227-237. [PMID: 29081003 DOI: 10.1007/s11064-017-2423-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/14/2017] [Accepted: 10/19/2017] [Indexed: 02/02/2023]
Abstract
Myelin protein zero (P0, MPZ) is the main cell adhesion molecule in peripheral myelin, the sequence of which is evolutionarily highly conserved. Large myelin protein zero (L-MPZ) is a novel translational readthrough molecule in mammals in a physiological status and is encoded by the P0 mRNA with an extra domain. The sequence similarities in the L-MPZ-specific region are found in humans and frogs but not in fish P0 cDNA. Actual synthesis of L-MPZ has been detected in rat and mouse sciatic nerve but not yet evaluated in frogs and humans. The production mechanism and physiological functions of L-MPZ remain unknown. Additionally, the sequence context around the canonical stop codon is significant for readthrough in viruses and yeast, but the correlation between the sequence around P0 stop codon and L-MPZ synthesis is unclear. Here, we focused on the phylogenetic pathways in L-MPZ synthesis. We have shown that L-MPZ is widely produced from frogs to humans using western blotting against L-MPZ. Mutation analysis of the sequence around the stop codon for L-MPZ synthesis using a mammalian in vitro transcription/translation system revealed that the evolutionarily conserved sequence around P0 stop codon is susceptible to readthrough and is similar to the consensus motif in viruses and yeast UAG stop codon type molecules. Our results demonstrate that the phylogenetically conserved sequence around the canonical P0 stop codon is essential for L-MPZ synthesis, suggesting that phylogenetic emergence of L-MPZ in amphibians may be related to particular distribution and/or function in the PNS myelin.
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Billon P, Bryant EE, Joseph SA, Nambiar TS, Hayward SB, Rothstein R, Ciccia A. CRISPR-Mediated Base Editing Enables Efficient Disruption of Eukaryotic Genes through Induction of STOP Codons. Mol Cell 2017; 67:1068-1079.e4. [PMID: 28890334 PMCID: PMC5610906 DOI: 10.1016/j.molcel.2017.08.008] [Citation(s) in RCA: 243] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/20/2017] [Accepted: 08/14/2017] [Indexed: 12/21/2022]
Abstract
Standard CRISPR-mediated gene disruption strategies rely on Cas9-induced DNA double-strand breaks (DSBs). Here, we show that CRISPR-dependent base editing efficiently inactivates genes by precisely converting four codons (CAA, CAG, CGA, and TGG) into STOP codons without DSB formation. To facilitate gene inactivation by induction of STOP codons (iSTOP), we provide access to a database of over 3.4 million single guide RNAs (sgRNAs) for iSTOP (sgSTOPs) targeting 97%-99% of genes in eight eukaryotic species, and we describe a restriction fragment length polymorphism (RFLP) assay that allows the rapid detection of iSTOP-mediated editing in cell populations and clones. To simplify the selection of sgSTOPs, our resource includes annotations for off-target propensity, percentage of isoforms targeted, prediction of nonsense-mediated decay, and restriction enzymes for RFLP analysis. Additionally, our database includes sgSTOPs that could be employed to precisely model over 32,000 cancer-associated nonsense mutations. Altogether, this work provides a comprehensive resource for DSB-free gene disruption by iSTOP.
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MESH Headings
- Animals
- Arabidopsis/genetics
- Arabidopsis/metabolism
- CRISPR-Associated Proteins/genetics
- CRISPR-Associated Proteins/metabolism
- CRISPR-Cas Systems
- Clustered Regularly Interspaced Short Palindromic Repeats
- Codon, Nonsense
- Codon, Terminator
- Computational Biology
- DNA Restriction Enzymes/genetics
- DNA Restriction Enzymes/metabolism
- Databases, Genetic
- Gene Editing/methods
- Gene Expression Regulation, Fungal
- Gene Expression Regulation, Neoplastic
- Gene Expression Regulation, Plant
- Gene Silencing
- HEK293 Cells
- Humans
- Mice
- Neoplasms/genetics
- Neoplasms/metabolism
- Polymorphism, Restriction Fragment Length
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Rats
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Transfection
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Affiliation(s)
- Pierre Billon
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Eric E Bryant
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Sarah A Joseph
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Tarun S Nambiar
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Samuel B Hayward
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Rodney Rothstein
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA.
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Frumkin J. Gentamicin, a read-through agent for the treatment of rectal cancer. Colorectal Dis 2017; 19:864. [PMID: 28755390 DOI: 10.1111/codi.13832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 06/14/2017] [Indexed: 02/08/2023]
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35
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Mucke HA. Drug Repurposing Patent Applications January–March 2017. Assay Drug Dev Technol 2017; 15:127-132. [DOI: 10.1089/adt.2017.29057.pq1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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36
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Richardson R, Smart M, Tracey-White D, Webster AR, Moosajee M. Mechanism and evidence of nonsense suppression therapy for genetic eye disorders. Exp Eye Res 2017; 155:24-37. [PMID: 28065590 DOI: 10.1016/j.exer.2017.01.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/24/2016] [Accepted: 01/04/2017] [Indexed: 01/09/2023]
Abstract
Between 5 and 70% of genetic disease is caused by in-frame nonsense mutations, which introduce a premature termination codon (PTC) within the disease-causing gene. Consequently, during translation, non-functional or gain-of-function truncated proteins of pathological significance, are formed. Approximately 50% of all inherited retinal disorders have been associated with PTCs, highlighting the importance of novel pharmacological or gene correction therapies in ocular disease. Pharmacological nonsense suppression of PTCs could delineate a therapeutic strategy that treats the mutation in a gene- and disease-independent manner. This approach aims to suppress the fidelity of the ribosome during protein synthesis so that a near-cognate aminoacyl-tRNA, which shares two of the three nucleotides of the PTC, can be inserted into the peptide chain, allowing translation to continue, and a full-length functional protein to be produced. Here we discuss the mechanisms and evidence of nonsense suppression agents, including the small molecule drug ataluren (or PTC124) and next generation 'designer' aminoglycosides, for the treatment of genetic eye disease.
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Affiliation(s)
- Rose Richardson
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, London, UK
| | - Matthew Smart
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, London, UK
| | - Dhani Tracey-White
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, London, UK
| | - Andrew R Webster
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Mariya Moosajee
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK.
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37
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Al-Jazrawe M, Au M, Alman B. Optimal therapy for desmoid tumors: current options and challenges for the future. Expert Rev Anticancer Ther 2015; 15:1443-58. [DOI: 10.1586/14737140.2015.1096203] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Evaluation of Aminoglycoside and Non-Aminoglycoside Compounds for Stop-Codon Readthrough Therapy in Four Lysosomal Storage Diseases. PLoS One 2015; 10:e0135873. [PMID: 26287674 PMCID: PMC4545610 DOI: 10.1371/journal.pone.0135873] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 07/27/2015] [Indexed: 11/21/2022] Open
Abstract
Nonsense mutations are quite prevalent in inherited diseases. Readthrough drugs could provide a therapeutic option for any disease caused by this type of mutation. Geneticin (G418) and gentamicin were among the first to be described. Novel compounds have been generated, but only a few have shown improved results. PTC124 is the only compound to have reached clinical trials. Here we first investigated the readthrough effects of gentamicin on fibroblasts from one patient with Sanfilippo B, one with Sanfilippo C, and one with Maroteaux-Lamy. We found that ARSB activity (Maroteaux-Lamy case) resulted in an increase of 2–3 folds and that the amount of this enzyme within the lysosomes was also increased, after treatment. Since the other two cases (Sanfilippo B and Sanfilippo C) did not respond to gentamicin, the treatments were extended with the use of geneticin and five non-aminoglycoside (PTC124, RTC13, RTC14, BZ6 and BZ16) readthrough compounds (RTCs). No recovery was observed at the enzyme activity level. However, mRNA recovery was observed in both cases, nearly a two-fold increase for Sanfilippo B fibroblasts with G418 and around 1.5 fold increase for Sanfilippo C cells with RTC14 and PTC124. Afterwards, some of the products were assessed through in vitro analyses for seven mutations in genes responsible for those diseases and, also, for Niemann-Pick A/B. Using the coupled transcription/translation system (TNT), the best results were obtained for SMPD1 mutations with G418, reaching a 35% recovery at 0.25 μg/ml, for the p.W168X mutation. The use of COS cells transfected with mutant cDNAs gave positive results for most of the mutations with some of the drugs, although to a different extent. The higher enzyme activity recovery, of around two-fold increase, was found for gentamicin on the ARSB p.W146X mutation. Our results are promising and consistent with those of other groups. Further studies of novel compounds are necessary to find those with more consistent efficacy and fewer toxic effects.
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Estrogen receptor β exon 3-deleted mouse: The importance of non-ERE pathways in ERβ signaling. Proc Natl Acad Sci U S A 2015; 112:5135-40. [PMID: 25848008 DOI: 10.1073/pnas.1504944112] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In 1998, an estrogen receptor β (ERβ) knockout (KO) mouse was created by interrupting the gene at the DNA binding domain (DBD) with a neocassette. The mutant females were subfertile and there were abnormalities in the brain, prostate, lung, colon, and immune system. In 2008, another ERβ mutant mouse was generated by deleting ERβ exon 3 which encodes the first zinc finger in the DBD. The female mice of this strain were unable to ovulate but were otherwise normal. The differences in the phenotypes of the two KO strains, have led to questions about the physiological function of ERβ. In the present study, we created an ERβ exon 3-deleted mouse (ERβ-Δex3) and confirmed that the only observable defect was anovulation. Despite the two in-frame stop codons introduced by splicing between exons 2 and 4, an ERβ protein was expressed in nuclei of prostate epithelial cells. Using two different anti-ERβ antibodies, we showed that an in-frame ligand binding domain and C terminus were present in the ERβ-Δex3 protein. Moreover, with nuclear extracts from ERβ-Δex3 prostates, there was an ERβ-dependent retardation of migration of activator protein-1 response elements in EMSA. Unlike the original knockout mouse, expression of Ki67, androgen receptor, and Dachshund-1 in prostate epithelium was not altered in the ERβ-Δex3 mouse. We conclude that very little of ERβ transcriptional activity depends on binding to classical estrogen response elements (EREs).
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Oliveira C, Pinheiro H, Figueiredo J, Seruca R, Carneiro F. Familial gastric cancer: genetic susceptibility, pathology, and implications for management. Lancet Oncol 2015; 16:e60-70. [PMID: 25638682 DOI: 10.1016/s1470-2045(14)71016-2] [Citation(s) in RCA: 252] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Familial gastric cancer comprises at least three major syndromes: hereditary diffuse gastric cancer, gastric adenocarcinoma and proximal polyposis of the stomach, and familial intestinal gastric cancer. The risk of development of gastric cancer is high in families affected b-y these syndromes, but only hereditary diffuse gastric cancer is genetically explained (caused by germline alterations of CDH1, which encodes E-cadherin). Gastric cancer is also associated with a range of several cancer-associated syndromes with known genetic causes, such as Lynch, Li-Fraumeni, Peutz-Jeghers, hereditary breast-ovarian cancer syndromes, familial adenomatous polyposis, and juvenile polyposis. We present contemporary knowledge on the genetics, pathogenesis, and clinical features of familial gastric cancer, and discuss research and technological developments, which together are expected to open avenues for new genetic testing approaches and novel therapeutic strategies.
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Affiliation(s)
- Carla Oliveira
- Ipatimub-Institute of Molecular Pathology and Immunology & Instituto Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal; Department of Pathology and Oncology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Hugo Pinheiro
- Ipatimub-Institute of Molecular Pathology and Immunology & Instituto Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
| | - Joana Figueiredo
- Ipatimub-Institute of Molecular Pathology and Immunology & Instituto Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
| | - Raquel Seruca
- Ipatimub-Institute of Molecular Pathology and Immunology & Instituto Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal; Department of Pathology and Oncology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Fátima Carneiro
- Ipatimub-Institute of Molecular Pathology and Immunology & Instituto Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal; Department of Pathology and Oncology, Faculty of Medicine, University of Porto, Porto, Portugal; Centro Hospitalar S João, Porto, Portugal.
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41
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Amaral MD. Novel personalized therapies for cystic fibrosis: treating the basic defect in all patients. J Intern Med 2015; 277:155-166. [PMID: 25266997 DOI: 10.1111/joim.12314] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cystic fibrosis (CF) is the most common genetic life-shortening condition in Caucasians. Despite being a multi-organ disease, CF is classically diagnosed by symptoms of acute/chronic respiratory disease, with persistent pulmonary infections and mucus plugging of the airways and failure to thrive. These multiple symptoms originate from dysfunction of the CF transmembrane conductance regulator (CFTR) protein, a channel that mediates anion transport across epithelia. Indeed, establishment of a definite CF diagnosis requires proof of CFTR dysfunction, commonly through the so-called sweat Cl(-) test. Many drug therapies, including mucolytics and antibiotics, aim to alleviate the symptoms of CF lung disease. However, new therapies to modulate defective CFTR, the basic defect underlying CF, have started to reach the clinic, and several others are in development or in clinical trials. The novelty of these therapies is that, besides targeting the basic defect underlying CF, they are mutation specific. Indeed, even this monogenic disease is influenced by a large number of different genes and biological pathways as well as by environmental factors that are difficult to assess. Accordingly, every person with CF is unique and so functional assessment of patients' tissues ex vivo is key for diagnosing and predicting the severity of this disease. Of note, such assessment will also be crucial to assess drug responses, in order to effectively treat all CF patients. It is not because it is a monogenic disorder that personalized treatment for CF is much easier than for complex disorders.
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Affiliation(s)
- M D Amaral
- BioFIG-Center for Biodiversity, Functional and Integrative Genomics, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
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42
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Oren YS, McClure ML, Rowe SM, Sorscher EJ, Bester AC, Manor M, Kerem E, Rivlin J, Zahdeh F, Mann M, Geiger T, Kerem B. The unfolded protein response affects readthrough of premature termination codons. EMBO Mol Med 2014; 6:685-701. [PMID: 24705877 PMCID: PMC4023889 DOI: 10.1002/emmm.201303347] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
One-third of monogenic inherited diseases result from premature termination codons (PTCs). Readthrough of in-frame PTCs enables synthesis of full-length functional proteins. However, extended variability in the response to readthrough treatment is found among patients, which correlates with the level of nonsense transcripts. Here, we aimed to reveal cellular pathways affecting this inter-patient variability. We show that activation of the unfolded protein response (UPR) governs the response to readthrough treatment by regulating the levels of transcripts carrying PTCs. Quantitative proteomic analyses showed substantial differences in UPR activation between patients carrying PTCs, correlating with their response. We further found a significant inverse correlation between the UPR and nonsense-mediated mRNA decay (NMD), suggesting a feedback loop between these homeostatic pathways. We uncovered and characterized the mechanism underlying this NMD-UPR feedback loop, which augments both UPR activation and NMD attenuation. Importantly, this feedback loop enhances the response to readthrough treatment, highlighting its clinical importance. Altogether, our study demonstrates the importance of the UPR and its regulatory network for genetic diseases caused by PTCs and for cell homeostasis under normal conditions.
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Affiliation(s)
- Yifat S Oren
- Department of Genetics, The Hebrew University, Jerusalem, Israel
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Aminoglycosides restore full-length type VII collagen by overcoming premature termination codons: therapeutic implications for dystrophic epidermolysis bullosa. Mol Ther 2014; 22:1741-52. [PMID: 25155989 DOI: 10.1038/mt.2014.140] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 07/16/2014] [Indexed: 11/08/2022] Open
Abstract
Patients with recessive dystrophic epidermolysis bullosa (RDEB) have severe, incurable skin fragility, blistering, and multiple skin wounds due to mutations in the gene encoding type VII collagen (C7), the major component of anchoring fibrils mediating epidermal-dermal adherence. Nearly 10-25% of RDEB patients carry nonsense mutations leading to premature stop codons (PTCs) that result in truncated C7. In this study, we evaluated the feasibility of using aminoglycosides to suppress PTCs and induce C7 expression in two RDEB keratinocyte cell lines (Q251X/Q251X and R578X/R906) and two primary RDEB fibroblasts (R578X/R578X and R163X/R1683X). Incubation of these cells with aminoglycosides (geneticin, gentamicin, and paromomycin) resulted in the synthesis and secretion of a full-length C7 in a dose-dependent and sustained manner. Importantly, aminoglycoside-induced C7 reversed the abnormal RDEB cell phenotype and incorporated into the dermal-epidermal junction of skin equivalents. We further demonstrated the general utility of aminoglycoside-mediated readthrough in 293 cells transiently transfected with expression vectors encoding 22 different RDEB nonsense mutations. This is the first study demonstrating that aminoglycosides can induce PTC readthrough and restore functional C7 in RDEB caused by nonsense mutations. Therefore, aminoglycosides may have therapeutic potential for RDEB patients and other inherited skin diseases caused by nonsense mutations.
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44
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Liu C, Karam R, Zhou Y, Su F, Ji Y, Li G, Xu G, Lu L, Wang C, Song M, Zhu J, Wang Y, Zhao Y, Foo WC, Zuo M, Valasek MA, Javle M, Wilkinson MF, Lu Y. The UPF1 RNA surveillance gene is commonly mutated in pancreatic adenosquamous carcinoma. Nat Med 2014; 20:596-8. [PMID: 24859531 PMCID: PMC4048332 DOI: 10.1038/nm.3548] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 03/27/2014] [Indexed: 12/15/2022]
Abstract
Pancreatic adenosquamous carcinoma (ASC) is an enigmatic and aggressive tumor that has a worse prognosis and higher metastatic potential than its adenocarcinoma counterpart. Here we report that ASC tumors frequently harbor somatically acquired mutations in the UPF1 gene, which encodes the core component of the nonsense-mediated RNA decay (NMD) pathway. These tumor-specific mutations alter UPF1 RNA splicing and perturb NMD, leading to upregulated levels of NMD substrate mRNAs. UPF1 mutations are, to our knowledge, the first known unique molecular signatures of pancreatic ASC.
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Affiliation(s)
- Chen Liu
- 1] Clinical and Translational Cancer Research Center, The Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China. [2] Tongji University School of Life Science and Technology, Shanghai, China. [3]
| | - Rachid Karam
- 1] Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, California, USA. [2]
| | - YingQi Zhou
- 1] The Third General Surgery Department, Changhai Hospital, Second Military Medical University, Shanghai, China. [2]
| | - Fang Su
- 1] Clinical and Translational Cancer Research Center, The Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China. [2]
| | - Yuan Ji
- 1] Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China. [2]
| | - Gang Li
- The Third General Surgery Department, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - GuoTong Xu
- Clinical and Translational Cancer Research Center, The Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - LiXia Lu
- Clinical and Translational Cancer Research Center, The Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - ChongRen Wang
- Clinical and Translational Cancer Research Center, The Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - MeiYi Song
- Clinical and Translational Cancer Research Center, The Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - JingPing Zhu
- Clinical and Translational Cancer Research Center, The Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - YiRan Wang
- Clinical and Translational Cancer Research Center, The Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - YiFan Zhao
- Clinical and Translational Cancer Research Center, The Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wai Chin Foo
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - MingXin Zuo
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mark A Valasek
- Division of Anatomic Pathology, Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Milind Javle
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Miles F Wilkinson
- 1] Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, California, USA. [2] Institute for Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - YanJun Lu
- Clinical and Translational Cancer Research Center, The Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
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Liu W, Mellado L, Espeso EA, Sealy-Lewis HM. In Aspergillus nidulans the suppressors suaA and suaC code for release factors eRF1 and eRF3 and suaD codes for a glutamine tRNA. G3 (BETHESDA, MD.) 2014; 4:1047-57. [PMID: 24727290 PMCID: PMC4065248 DOI: 10.1534/g3.114.010702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 03/25/2014] [Indexed: 11/24/2022]
Abstract
In Aspergillus nidulans, after extensive mutagenesis, a collection of mutants was obtained and four suppressor loci were identified genetically that could suppress mutations in putative chain termination mutations in different genes. Suppressor mutations in suaB and suaD have a similar restricted spectrum of suppression and suaB111 was previously shown to be an alteration in the anticodon of a gln tRNA. We have shown that like suaB, a suaD suppressor has a mutation in the anticodon of another gln tRNA allowing suppression of UAG mutations. Mutations in suaA and suaC had a broad spectrum of suppression. Four suaA mutations result in alterations in the coding region of the eukaryotic release factor, eRF1, and another suaA mutation has a mutation in the upstream region of eRF1 that prevents splicing of the first intron within the 5'UTR. Epitope tagging of eRF1 in this mutant results in 20% of the level of eRF1 compared to the wild-type. Two mutations in suaC result in alterations in the eukaryotic release factor, eRF3. This is the first description in Aspergillus nidulans of an alteration in eRF3 leading to suppression of chain termination mutations.
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Affiliation(s)
- Wen Liu
- Department of Biological, Biomedical and Environmental Sciences, University of Hull, Hull HU6 7RX, United Kingdom
| | - Laura Mellado
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Eduardo A Espeso
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Heather M Sealy-Lewis
- Department of Biological, Biomedical and Environmental Sciences, University of Hull, Hull HU6 7RX, United Kingdom
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Micale L, Augello B, Maffeo C, Selicorni A, Zucchetti F, Fusco C, De Nittis P, Pellico MT, Mandriani B, Fischetto R, Boccone L, Silengo M, Biamino E, Perria C, Sotgiu S, Serra G, Lapi E, Neri M, Ferlini A, Cavaliere ML, Chiurazzi P, Monica MD, Scarano G, Faravelli F, Ferrari P, Mazzanti L, Pilotta A, Patricelli MG, Bedeschi MF, Benedicenti F, Prontera P, Toschi B, Salviati L, Melis D, Di Battista E, Vancini A, Garavelli L, Zelante L, Merla G. Molecular analysis, pathogenic mechanisms, and readthrough therapy on a large cohort of Kabuki syndrome patients. Hum Mutat 2014; 35:841-50. [PMID: 24633898 PMCID: PMC4234006 DOI: 10.1002/humu.22547] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/05/2014] [Indexed: 12/04/2022]
Abstract
Kabuki syndrome (KS) is a multiple congenital anomalies syndrome characterized by characteristic facial features and varying degrees of mental retardation, caused by mutations in KMT2D/MLL2 and KDM6A/UTX genes. In this study, we performed a mutational screening on 303 Kabuki patients by direct sequencing, MLPA, and quantitative PCR identifying 133 KMT2D, 62 never described before, and four KDM6A mutations, three of them are novel. We found that a number of KMT2D truncating mutations result in mRNA degradation through the nonsense-mediated mRNA decay, contributing to protein haploinsufficiency. Furthermore, we demonstrated that the reduction of KMT2D protein level in patients’ lymphoblastoid and skin fibroblast cell lines carrying KMT2D-truncating mutations affects the expression levels of known KMT2D target genes. Finally, we hypothesized that the KS patients may benefit from a readthrough therapy to restore physiological levels of KMT2D and KDM6A proteins. To assess this, we performed a proof-of-principle study on 14 KMT2D and two KDM6A nonsense mutations using specific compounds that mediate translational readthrough and thereby stimulate the re-expression of full-length functional proteins. Our experimental data showed that both KMT2D and KDM6A nonsense mutations displayed high levels of readthrough in response to gentamicin treatment, paving the way to further studies aimed at eventually treating some Kabuki patients with readthrough inducers.
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Affiliation(s)
- Lucia Micale
- Medical Genetics Unit, IRCCS Casa Sollievo Della Sofferenza Hospital, San Giovanni Rotondo, Italy
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47
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Lentini L, Melfi R, Di Leonardo A, Spinello A, Barone G, Pace A, Palumbo Piccionello A, Pibiri I. Toward a rationale for the PTC124 (Ataluren) promoted readthrough of premature stop codons: a computational approach and GFP-reporter cell-based assay. Mol Pharm 2014; 11:653-64. [PMID: 24483936 PMCID: PMC4167060 DOI: 10.1021/mp400230s] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 12/17/2013] [Accepted: 01/31/2014] [Indexed: 01/28/2023]
Abstract
The presence in the mRNA of premature stop codons (PTCs) results in protein truncation responsible for several inherited (genetic) diseases. A well-known example of these diseases is cystic fibrosis (CF), where approximately 10% (worldwide) of patients have nonsense mutations in the CF transmembrane regulator (CFTR) gene. PTC124 (3-(5-(2-fluorophenyl)-1,2,4-oxadiazol-3-yl)-benzoic acid), also known as Ataluren, is a small molecule that has been suggested to allow PTC readthrough even though its target has yet to be identified. In the lack of a general consensus about its mechanism of action, we experimentally tested the ability of PTC124 to promote the readthrough of premature termination codons by using a new reporter. The reporter vector was based on a plasmid harboring the H2B histone coding sequence fused in frame with the green fluorescent protein (GFP) cDNA, and a TGA stop codon was introduced in the H2B-GFP gene by site-directed mutagenesis. Additionally, an unprecedented computational study on the putative supramolecular interaction between PTC124 and an 11-codon (33-nucleotides) sequence corresponding to a CFTR mRNA fragment containing a central UGA nonsense mutation showed a specific interaction between PTC124 and the UGA codon. Altogether, the H2B-GFP-opal based assay and the molecular dynamics (MD) simulation support the hypothesis that PTC124 is able to promote the specific readthrough of internal TGA premature stop codons.
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Affiliation(s)
- Laura Lentini
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Raffaella Melfi
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Aldo Di Leonardo
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
- Centro di OncoBiologia
Sperimentale (COBS), via San Lorenzo
Colli, 90145 Palermo, Italy
| | - Angelo Spinello
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Giampaolo Barone
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
- Istituto EuroMediterraneo
di Scienza e Tecnologia (IEMEST), Via
Emerico Amari 123, 90139 Palermo, Italy
| | - Andrea Pace
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
- Istituto EuroMediterraneo
di Scienza e Tecnologia (IEMEST), Via
Emerico Amari 123, 90139 Palermo, Italy
| | - Antonio Palumbo Piccionello
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Ivana Pibiri
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
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48
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Realizing the promise of cancer predisposition genes. Nature 2014; 505:302-8. [PMID: 24429628 DOI: 10.1038/nature12981] [Citation(s) in RCA: 416] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 11/21/2013] [Indexed: 12/14/2022]
Abstract
Genes in which germline mutations confer highly or moderately increased risks of cancer are called cancer predisposition genes. More than 100 of these genes have been identified, providing important scientific insights in many areas, particularly the mechanisms of cancer causation. Moreover, clinical utilization of cancer predisposition genes has had a substantial impact on diagnosis, optimized management and prevention of cancer. The recent transformative advances in DNA sequencing hold the promise of many more cancer predisposition gene discoveries, and greater and broader clinical applications. However, there is also considerable potential for incorrect inferences and inappropriate clinical applications. Realizing the promise of cancer predisposition genes for science and medicine will thus require careful navigation.
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49
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Bordeira-Carriço R, Ferreira D, Mateus DD, Pinheiro H, Pêgo AP, Santos MAS, Oliveira C. Rescue of wild-type E-cadherin expression from nonsense-mutated cancer cells by a suppressor-tRNA. Eur J Hum Genet 2014; 22:1085-92. [PMID: 24424122 DOI: 10.1038/ejhg.2013.292] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Revised: 11/12/2013] [Accepted: 11/20/2013] [Indexed: 02/07/2023] Open
Abstract
Hereditary diffuse gastric cancer (HDGC) syndrome, although rare, is highly penetrant at an early age, and is severe and incurable because of ineffective screening tools and therapy. Approximately 45% of HDGC families carry germline CDH1/E-cadherin alterations, 20% of which are nonsense leading to premature protein truncation. Prophylactic gastrectomy is the only recommended approach for all asymptomatic CDH1 mutation carriers. Suppressor-tRNAs can replace premature stop codons (PTCs) with a cognate amino acid, inducing readthrough and generating full-length proteins. The use of suppressor-tRNAs in HDGC patients could therefore constitute a less invasive therapeutic option for nonsense mutation carriers, delaying the development of gastric cancer. Our analysis revealed that 23/108 (21.3%) of E-cadherin-mutant families carried nonsense mutations that could be potentially corrected by eight suppressor-tRNAs, and arginine was the most frequently affected amino acid. Using site-directed mutagenesis, we developed an arginine suppressor-tRNA vector to correct one HDGC nonsense mutation. E-cadherin- deficient cell lines were transfected with plasmids carrying simultaneously the suppressor-tRNA and wild-type or mutant CDH1 mini-genes. RT-PCR, western blot, immunofluorescence, flow cytometry and proximity ligation assay (PLA) were used to establish the model, and monitor mRNA and protein expression and function recovery from CDH1 vectors. Cells expressing a CDH1 mini-gene, carrying a nonsense mutation and the suppressor-tRNA, recovered full-length E-cadherin expression and its correct localization and incorporation into the adhesion complex. This is the first demonstration of functional recovery of a mutated causative gene in hereditary cancer by cognate amino acid replacement with suppressor-tRNAs. Of the HDGC families, 21.3% are candidates for correction with suppressor-tRNAs to potentially delay cancer onset.
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Affiliation(s)
- Renata Bordeira-Carriço
- Expression Regulation in Cancer Group, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Daniel Ferreira
- Expression Regulation in Cancer Group, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Denisa D Mateus
- Expression Regulation in Cancer Group, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Hugo Pinheiro
- Expression Regulation in Cancer Group, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Ana Paula Pêgo
- 1] INEB, Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal [2] Universidade do Porto-Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Porto, Portugal [3] Universidade do Porto-Faculdade de Engenharia, Porto, Portugal
| | - Manuel A S Santos
- RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Carla Oliveira
- 1] Expression Regulation in Cancer Group, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal [2] Faculty of Medicine of the University of Porto, Porto, Portugal
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Abstract
It is becoming increasingly clear that genomics is beginning to have a major impact in guiding diagnoses and treatment of many disorders. As the cost of DNA sequencing continues to drop and more patient genomes are sequenced, the challenge is to deliver this knowledge to the clinic, particularly in cancer. DNA sequencing of patients with rare disease is revealing novel druggable pathways for more common disorders. Genetic tools for treating disease are also advancing rapidly. Genetic approaches, thought to be pipedreams five years ago for diseases such as Duchenne muscular dystrophy, are now showing promise in clinical trials and many of these methodologies are being applied more widely for other diseases. The era of genomic medicine has arrived.
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